LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# Simple rigid body system

units		lj
atom_style	atomic

pair_style	lj/cut 2.5

read_data	data.rigid
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  81 atoms

velocity 	all create 100.0 4928459

# unconnected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 10 18
#group		clump3 id <> 19 27
#group		clump4 id <> 28 36
#group		clump5 id <> 37 45
#group		clump6 id <> 46 54
#group		clump7 id <> 55 63
#group		clump8 id <> 64 72
#group		clump9 id <> 73 81

#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 #	  	      clump6 clump7 clump8 clump9

# 1 chain of connected bodies

group		clump1 id <> 1 9
9 atoms in group clump1
group		clump2 id <> 9 18
10 atoms in group clump2
group		clump3 id <> 18 27
10 atoms in group clump3
group		clump4 id <> 27 36
10 atoms in group clump4
group		clump5 id <> 36 45
10 atoms in group clump5
group		clump6 id <> 45 54
10 atoms in group clump6
group		clump7 id <> 54 63
10 atoms in group clump7
group		clump8 id <> 63 72
10 atoms in group clump8
group		clump9 id <> 72 81
10 atoms in group clump9

fix 1 all poems group clump1 clump2 clump3 clump4 clump5 	  	      clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms

# 2 chains of connected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 9 18
#group		clump3 id <> 18 27
#group		clump4 id <> 27 36
#group		clump5 id <> 37 45
#group		clump6 id <> 45 54
#group		clump7 id <> 54 63
#group		clump8 id <> 63 72
#group		clump9 id <> 72 81

#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9

neigh_modify	exclude group clump1 clump1
neigh_modify	exclude group clump2 clump2
neigh_modify	exclude group clump3 clump3
neigh_modify	exclude group clump4 clump4
neigh_modify	exclude group clump5 clump5
neigh_modify	exclude group clump6 clump6
neigh_modify	exclude group clump7 clump7
neigh_modify	exclude group clump8 clump8
neigh_modify	exclude group clump9 clump9

thermo		100

#dump		1 all atom 50 dump.rigid.poems

#dump		2 all image 100 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30
#dump_modify	2 pad 5

#dump		3 all movie 100 movie.mpg type type #		axes yes 0.8 0.02 view 60 -30
#dump_modify	3 pad 5

timestep 	0.0001
thermo		50
run		10000
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 18 18 18
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.292 | 3.292 | 3.292 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0     217.7783    3430.3907            0    3466.6871   -2.7403788 
      50    13679.637    1404.2468            0    3684.1863    12.446066 
     100    16777.225    888.87665            0    3685.0808   -31.828677 
     150    19595.365    418.45042            0    3684.3446    40.709078 
     200    18524.188    596.47273            0    3683.8375   -0.8159371 
     250    21015.789    180.96521            0    3683.5967   -10.042469 
     300    20785.513    219.25314            0    3683.5053    2.6452719 
     350     21072.46     171.2554            0    3683.3321    7.0609024 
     400    19956.414    356.36381            0    3682.4328    19.320259 
     450     20724.42    227.73284            0    3681.8028    8.1259249 
     500    20152.578    322.71466            0    3681.4777    5.4929878 
     550    20017.022    345.29701            0    3681.4673    5.4661666 
     600    17897.743    698.72196            0    3681.6791    3.2854742 
     650    17297.758    796.60256            0    3679.5623    15.191113 
     700    18581.934    584.29715            0    3681.2861    5.1588289 
     750    21774.158    52.821062            0    3681.8474   -10.775664 
     800    21604.055    81.188546            0    3681.8644   -3.2045743 
     850    17821.483    711.53827            0    3681.7854    7.4384277 
     900    21033.292    175.98127            0    3681.5299   -16.345167 
     950    20968.166    186.59847            0    3681.2929    -2.330456 
    1000     20490.66    266.19375            0    3681.3037    11.787983 
    1050    20222.396    310.94072            0      3681.34   -8.3459539 
    1100    21321.687    127.61533            0    3681.2299   -1.2184717 
    1150    20849.582    206.01695            0    3680.9472  -0.86699149 
    1200    21815.003    45.317414            0    3681.1512    1.5988314 
    1250    18655.437    572.41453            0     3681.654    10.064078 
    1300    20780.781    217.36506            0    3680.8286    6.0538616 
    1350    20558.971    254.36482            0    3680.8601   -3.6773952 
    1400    21485.029    99.812921            0    3680.6511   -16.185473 
    1450    21771.107     52.15961            0    3680.6775   -2.4756673 
    1500    21520.948    93.503927            0    3680.3286    2.1023576 
    1550    21351.418    121.68137            0    3680.2511    5.5159947 
    1600    20778.805    216.92177            0    3680.0559    15.089188 
    1650    21477.638    100.21836            0    3679.8247   -1.1045746 
    1700    18501.339    596.47914            0    3680.0357   -15.679679 
    1750    18563.642    587.34785            0    3681.2882    33.532209 
    1800    19110.185     494.8234            0    3679.8543    18.024046 
    1850    21364.191    119.23545            0    3679.9339    2.5291103 
    1900    20146.626    322.14867            0    3679.9197    5.7313218 
    1950    20692.672    231.25325            0    3680.0319    4.2977763 
    2000    20943.904    189.11235            0    3679.7629   -22.645121 
    2050    19668.057    401.82994            0    3679.8394    3.6251916 
    2100    20280.442    299.76155            0    3679.8353    7.4807949 
    2150     19181.86      483.522            0    3680.4987    22.620507 
    2200    21300.161    130.70534            0    3680.7322    4.7102665 
    2250    20486.943    266.63931            0    3681.1299   -8.6456512 
    2300    18653.122    572.24819            0    3681.1018   -5.2637122 
    2350    21513.523    95.614901            0    3681.2021   -9.3621767 
    2400    21466.272    103.56446            0    3681.2765   -29.561368 
    2450    20100.105    332.27123            0    3682.2887    35.744287 
    2500    20764.395     221.6677            0    3682.4001   -12.468906 
    2550    20435.699    276.31055            0    3682.2603   -22.413697 
    2600    21466.467    104.53618            0    3682.2807   -10.078508 
    2650    20814.737    213.23892            0    3682.3617    5.1390411 
    2700    18565.761     588.3578            0    3682.6513     22.27664 
    2750     20772.36     220.1607            0    3682.2206   -7.9448198 
    2800    21018.563    179.10058            0    3682.1945   -7.0717829 
    2850    16789.412    884.21472            0    3682.4501    33.279015 
    2900    19304.363    464.75282            0    3682.1466     7.947554 
    2950    20513.758    263.07578            0    3682.0355    2.2361434 
    3000    20617.309    245.95251            0    3682.1706  -0.75213689 
    3050     18567.52    587.90473            0    3682.4914   -4.0112006 
    3100    18696.577    566.20617            0    3682.3023   -1.4814167 
    3150    19864.606    371.56078            0    3682.3284    8.9362836 
    3200    18902.643    532.04614            0    3682.4867   0.76630303 
    3250    21110.454    163.86212            0     3682.271   -1.6253894 
    3300    19369.939    454.05833            0    3682.3816    4.9066544 
    3350    19082.603    501.69905            0     3682.133    3.5982292 
    3400    19527.779      426.918            0    3681.5478    6.9612143 
    3450    19892.953    366.19989            0    3681.6921    3.0050426 
    3500    19708.981    396.84552            0    3681.6756    7.0757635 
    3550    20256.096    306.23937            0    3682.2554    -1.752138 
    3600    21289.889    133.93823            0     3682.253   -3.7462615 
    3650    18333.877    627.18028            0    3682.8264   -15.276791 
    3700    19829.133    377.33753            0    3682.1931    -6.269648 
    3750    20771.635    220.07171            0    3682.0109   -28.479036 
    3800    18373.813    619.79253            0    3682.0947    29.594781 
    3850     19320.99    461.92786            0    3682.0928   -5.3212101 
    3900    16119.825    995.68064            0    3682.3182   -8.4683118 
    3950    15556.948    1091.3655            0    3684.1902     20.98273 
    4000    20000.464    348.24891            0    3681.6596    7.1589745 
    4050    18870.219    536.59924            0    3681.6358   -3.7997025 
    4100    19889.518    367.49253            0    3682.4122   -14.091266 
    4150    15789.623    1051.3399            0    3682.9438   -4.4152389 
    4200    20548.889    256.83493            0    3681.6498   0.92234153 
    4250    20681.925    235.46113            0    3682.4487   -11.515773 
    4300    19330.404    460.80975            0    3682.5437   -22.351775 
    4350    19369.443    453.35405            0    3681.5945    29.418242 
    4400    20762.165    222.24133            0    3682.6021    2.6627047 
    4450    19984.657    350.71294            0    3681.4891     28.88731 
    4500     21167.58    154.25344            0    3682.1834   -3.0784322 
    4550    18133.576    660.73671            0    3682.9995    2.5305835 
    4600    19935.069    360.36826            0    3682.8798    2.4575034 
    4650     21413.76    113.86464            0    3682.8246   -5.1271547 
    4700    21716.333    63.609419            0    3682.9982   -2.4708049 
    4750    21352.947    124.36961            0    3683.1941  -0.29026265 
    4800    19043.788     508.8617            0    3682.8264    14.797006 
    4850    20516.121    263.78758            0    3683.1411    7.1348281 
    4900      20624.5    245.81827            0     3683.235   0.34708051 
    4950    20317.197    296.68937            0    3682.8889  -0.55065946 
    5000    18346.865    625.37246            0    3683.1832    7.3371413 
    5050     18867.53    538.49153            0    3683.0799    1.9249866 
    5100    18790.276    551.17224            0     3682.885    2.2333017 
    5150    20241.365    311.84683            0    3685.4076    -3.998004 
    5200    17685.058    739.76418            0    3687.2739    3.2835025 
    5250    18496.626    604.58166            0    3687.3526   -10.185776 
    5300    18420.042    617.82026            0    3687.8273   -16.392458 
    5350    18767.338     559.0349            0    3686.9246    4.5320767 
    5400    20423.245    284.90517            0    3688.7794   -8.6356656 
    5450    21080.398    176.18494            0    3689.5846   -16.450038 
    5500    16684.424    909.12643            0    3689.8637     49.94555 
    5550     20132.31    335.03663            0    3690.4216   -16.018038 
    5600    20430.923    285.17562            0    3690.3295   -5.0773675 
    5650    20479.943    276.55962            0    3689.8834    5.4334564 
    5700    20061.532    345.95553            0    3689.5441   -16.230658 
    5750    20523.759    268.92217            0    3689.5487   -4.4128812 
    5800    18900.356    537.65462            0    3687.7139    13.605549 
    5850    20280.502    310.27193            0    3690.3556   -4.7884959 
    5900     19050.26    515.66087            0    3690.7042    7.8864722 
    5950    19566.917     430.2997            0    3691.4525    31.715268 
    6000    18878.118    544.75449            0    3691.1076   -4.2415329 
    6050    19308.682    471.70734            0     3689.821   -10.561614 
    6100    18776.194    560.04764            0    3689.4133   -7.7286747 
    6150    21475.064     110.1508            0    3689.3281   -3.6506391 
    6200        19975    360.82675            0    3689.9934    10.282021 
    6250    21396.341     123.5341            0    3689.5909   -5.7215163 
    6300    18533.423    600.87422            0     3689.778    15.408027 
    6350    20653.152    247.19253            0    3689.3846    8.5607784 
    6400    19716.537    403.41487            0    3689.5044    13.165575 
    6450     21120.66    168.79838            0    3688.9084  -0.50382728 
    6500    19700.345     404.7155            0    3688.1064    13.941375 
    6550    10818.393     1892.037            0    3695.1025    38.423155 
    6600    18684.478    574.84755            0    3688.9273    5.9176985 
    6650    19219.732    486.04269            0    3689.3314    18.287659 
    6700    20058.587    344.88255            0    3687.9804    6.5372086 
    6750    21279.318    142.77333            0    3689.3264     2.498188 
    6800    20671.545    244.25024            0    3689.5078   -4.1356416 
    6850    21203.598    155.82001            0     3689.753 -0.0083061182 
    6900    21699.344    73.301497            0    3689.8588   -8.0309898 
    6950    20951.212    197.19403            0    3689.0627   0.76668303 
    7000    20166.275    329.02869            0    3690.0746    2.0083318 
    7050    21554.944    97.465792            0    3689.9564   -3.2420086 
    7100    20817.494    220.25476            0    3689.8372   0.17206182 
    7150     21481.11    109.84029            0    3690.0253   -3.6814741 
    7200    21266.824    145.53099            0    3690.0016    -2.060543 
    7250    19434.684    450.81331            0    3689.9273    9.4822765 
    7300    21246.525    148.96573            0    3690.0532    3.3208839 
    7350    19749.269    398.60049            0    3690.1454    1.0929662 
    7400    20354.792    297.70261            0     3690.168     1.547159 
    7450    19996.859    357.16723            0     3689.977  -0.68412025 
    7500    20179.628    326.53243            0    3689.8038   -2.4805507 
    7550    18765.184    561.65039            0    3689.1811   -1.7976428 
    7600    19457.496    447.04428            0    3689.9603   -1.9055522 
    7650    18206.823    655.57276            0    3690.0433    1.2797964 
    7700    19152.344    497.77422            0    3689.8315    18.145069 
    7750    21387.484    125.48654            0    3690.0673   -2.9915772 
    7800    18127.052    668.61425            0    3689.7896     9.044869 
    7850    21419.557    120.08889            0     3690.015    6.2651717 
    7900    21817.182    53.739819            0    3689.9368   -4.2387416 
    7950    18215.195    654.15494            0    3690.0208   -54.628049 
    8000    21523.503    102.58018            0    3689.8307     -4.84236 
    8050    20720.799    236.28689            0    3689.7535   -9.3725225 
    8100    21196.483     157.3232            0    3690.0704   -7.7222497 
    8150    20869.667    211.65308            0    3689.9309   -6.8438295 
    8200    17790.052    725.72497            0    3690.7336   -25.697688 
    8250     19634.94    417.71929            0    3690.2094     8.861604 
    8300    19135.784    500.92443            0    3690.2218   -3.1245167 
    8350    20191.718    324.93312            0    3690.2195    6.5736107 
    8400    20695.239    241.02378            0    3690.2302   -14.592221 
    8450    21793.857    57.609525            0    3689.9191   -11.509747 
    8500    21271.088    144.43102            0    3689.6124 -0.091587085 
    8550    20064.337    345.21754            0    3689.2737    9.5058471 
    8600     20282.86     308.2307            0    3688.7074     2.265529 
    8650    21223.055    151.24306            0     3688.419    1.7296834 
    8700    18875.342    542.42055            0    3688.3108     6.367148 
    8750     20922.65    201.55122            0    3688.6595    3.4208578 
    8800     21406.54     120.8539            0    3688.6106    1.8253729 
    8850    19868.524    377.05623            0     3688.477    16.327796 
    8900    20025.322    348.94892            0    3686.5025    17.063406 
    8950    21224.374     151.3567            0    3688.7524  -0.11028753 
    9000    21318.309      135.862            0    3688.9135  -0.50826819 
    9050    17538.618    768.00136            0    3691.1043    37.978645 
    9100    21247.861    147.84641            0    3689.1566   -6.7773259 
    9150    18455.677    613.08767            0    3689.0339   -3.4844751 
    9200    19486.859    441.03829            0    3688.8482   -18.602827 
    9250    21774.926    59.710446            0    3688.8648   -13.379919 
    9300    17628.877    750.72321            0    3688.8694    27.797974 
    9350    19827.334    383.85708            0    3688.4128    6.5459021 
    9400    20020.126    351.61742            0    3688.3051   -14.332562 
    9450    21596.338    88.904175            0    3688.2939    1.5779716 
    9500    18981.418    524.60141            0    3688.1711    5.4352409 
    9550    18652.616    579.05144            0    3687.8208    25.600729 
    9600    21198.037    155.23097            0    3688.2371   -3.3586596 
    9650    19958.317    361.32544            0    3687.7115    4.2910178 
    9700    19129.101     499.5993            0    3687.7828    13.267102 
    9750    21913.967    35.689587            0    3688.0174   -7.3222905 
    9800    21314.694    135.43794            0    3687.8869   -9.5613518 
    9850    20899.743    204.82802            0    3688.1185   -2.6321428 
    9900    20288.244     306.5013            0    3687.8753    3.6196618 
    9950    19271.015    475.88527            0    3687.7211   -1.8196764 
   10000     21122.24    167.82714            0    3688.2005   -3.8464842 
Loop time of 6.61148 on 1 procs for 10000 steps with 81 atoms

Performance: 13068.179 tau/day, 1512.521 timesteps/s
97.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.14595    | 0.14595    | 0.14595    |   0.0 |  2.21
Neigh   | 0.10704    | 0.10704    | 0.10704    |   0.0 |  1.62
Comm    | 0.013317   | 0.013317   | 0.013317   |   0.0 |  0.20
Output  | 0.0047956  | 0.0047956  | 0.0047956  |   0.0 |  0.07
Modify  | 6.3318     | 6.3318     | 6.3318     |   0.0 | 95.77
Other   |            | 0.008603   |            |       |  0.13

Nlocal:    81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    744 ave 744 max 744 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 744
Ave neighs/atom = 9.18519
Neighbor list builds = 992
Dangerous builds = 941

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:06
